Describe the numerical abundance of microbial life in relation to ecology and biogeochemistry of Earth systems.
What were the main questions being asked?
There are two main questions that are asked in this article. One of the main questions that is asked is the estimated number of prokaryotes in the different environments including aquatic, soil, oceanic and terrestrial subsurfaces. Second, the article also asks hows much cellular carbon prokaryotes contribute to the total amount of carbon on Earth.
What were the primary methodological approaches used?
To calculate the number of prokaryotes in the oceanic reservoir, polar region and frewshwater/saline lakes, cellular density was multiplied to global estimates of ocean/lake volume to determine the total number of cells. For the polar region, data from existing literature was used for the estimated number of prokaryotes and they used mean area extent of seasonal ice. To calculate prokaryotes in the soil, cellular density was measured using dfirect counts from forest soil and past field studies. These values were used in addition to previously estimated amounts of soil on Earth to calculate the total prokaryotic abundance in the soil. To calculate the number of prokaryotes in the terrestrial subsurface they estimated the number of prokaryotes in groundwater based on values from several sites. These values were multiplied using the estimated value of groundwater on Earth. In addition, they also did a separate calculation using the average porosity of Earth’s soil and used known values of space occupied by prokaryotes within these pores. To calculate the carbon content and prduction by prokaryotes, the dry weight of cells was first calculated. Two important assumptions were made, first It was assumed that the amount of carbon in prokaryotes was equal to half of their dry weight. Second, it was assumed that the amount of carbon produced during each turnover is about four times their carbon content. These two assumptions and the prokaryotic turnover rates were used to calculate the production of carbon in prokaryotes.
Summarize the main results or findings.
It was found that prokaryotes do the most primary productivity in the ocean. Prokaryotes have the capacity for genetic diversity as they can evolve. Prokaryotic carbon globally, is almost double the total carbon in living organisms. Based on oceanic, soil and oceanic and terrestrial subsurface habitats, the estimated total number of prokaryotes is 4.6x10^30 cells. Prokaryotes contribute 350-550pg carbon to the total amount of carbon on Earth and this is assumed to double the current estimates of carbons stored in living organisms. The total amount of prokaryotic carbon is 60-100% of the estimated total carbon in plants. Prokaryotes contain about 85-130Pg of nitrogen and 9-14Pg of phosphorous, which is almost 10 fold more than plants. Most of the prokaryotes are found in the ocean, soil, and oceanic and terrestrial subsurface habitats: 1.2x10^29 cells in open ocean, 2.6x10^29 cells in soil, 3.5x10^30 cells in oceanic subsurface, 0.25-2.5) x 10^30 cells in terrestrial subsurface. The cellular production rate is about 1.7x10^30 cells/year.The average prokaryotic turnover times are: -1.2x10^29 cells in open ocean -2.6x10^29 cells in soil -3.5x10^30 cells in oceanic subsurface -(0.25-2.5) x 10^30 cells in terrestrial subsurface
Comment on the emergence of microbial life and the evolution of Earth systems
Indicate the key events in the evolution of Earth systems at tic marks. Describe the dominant physical and chemical characteristics of Earth systems at waypoints.
Hadean
4.6 GA: Solar system formed, inner planets received water vapor and carbon. Increased CO2 and P vapour.
4.5 GA: Moon formed and gave Earth spin and tilt, day/night cycle, and seasons. Temperature dropped to 100 degrees celcius.
4.5 GA – 4.1 GA: High levels of CO2, increased temperature during times of the weak and early sun.
4.4 GA: Zircon formation: oldest mineral 4.4 GA – 4,1 GA: Meteorite impacts
4.1 GA: Evidence of life in zircon and from carbon isotopes
4 GA: Oldest rock: Acasta gneiss and evidence of plate subduction
Archaean
3.8 GA: Existence of life: from sedimentary rocks and methanogenesis. Meteorite bombardment halted. Sulphur reduction began. Rubisco catalyzing the fixation of nitrogen.
3.6 GA: Methanogenesis: the sun was very dim and without greenhouse gasses the Earth would have frozen.
3.5 GA: Microfossils and stromatolites present
3.5 GA – 2.7GA: Cyanobacteria photosynthesize
2.7 GA: Great oxidation event: responsible for glaciation. Evidence of eukaryotes. Another glaciation around 3.0GA.
Proterozoic
2.5 GA – 1.5 GA: red rock beds observed: evidence of oxidation
2.2 GA: O2 levels increase sharply which allowed for emergence of complex eukaryotes and micro aerobic early atmosphere –> oxic air. Cellular cybernetic switch between mitochondria and chloroplasts which may control the link between photsynthesis, CO2 and nitrogen fixation.
1.7 GA: Eukaryotes appear
1.1 GA: Snowball Earth occurs
Phanerozoic
540 MA: Cambrian explosion: increased diversity of life and larger organisms. Animals emerged
400 MA: Clevonian explosion: Land plants emerged, increased oxygenation of atmosphere
250 MA: Permian extinction: 95% species extinct
Gigantism of organisms
65 MA: Cretaceous/Paleogene Extinction
Describe the dominant physical and chemical characteristics of Earth systems at waypoints.
Hadean
There was a lot of CO2 to keep the Earth warm, as the sun was weak back then. Earth was mostly molten rock and very hot.
Archean
Atmosphere was filled with CH4 to keep the Earth warm still. As photosynthesis evolved, some O2 was present.
Proterozoic
O2 reacted with atmospheric methane to produce CO2. This caused a net decrease in greenhouse gas effects, making earth cold and leading to glaciation. Oxygen on Earth started oxidizing iron into banded iron formations, seen in sedimentary rock.
Phanerozoic
Plants started to evolve and can be seen on Earth. Coal deposits developed as organisms died in extinctions and were stored in sediments. There was the occasional glaciation periods
Evaluate human impacts on the ecology and biogeochemistry of Earth systems
What were the main questions being asked
The main questions that were being asked were: What “planetary boundaries” define the safe operating space for humanity with respect to the Earth? What “planetary boundaries” are associated with Earth’s biophysical processes? What are the Earth-system processes and associated thresholds? Can these generate unacceptable environmental change? How close is human society from reaching these thresholds in different Earth systems?
What were the primary methodological approaches used?
To determine climate change sediments and ice cores were used to measure greenhouse gas levels in the past. To determine biodiversity loss, fossil records were used to compare extinction rates. they also used the changes in climate, vegetation and land over the years to study the change in biodiversity. To study the nitrogen and phosphorus cycles they used water sampling. They studied the amount of fertilizer that was used to determine the amount of nitrogen that was added to the atmosphere by humans. They also defined the boundary of N-levles by saying that human fixation of N2 from the atmosphere was a big ‘valve’ which was responsible for the flow of nitrogen.
Summarize the main results or findings.
The article states that climate change, rate of biodiversity loss and the changes in the nitrogen cycle is what has caused the planetary boundaries to change as the threshold has been surpassed. Humans are thought to be the main cause for changes in climate change as we are continuously interfering with the biogeochemical cycles such as the nitrogen cycle. Atmospheric CO2 concentration should not typically exceed 350 ppm as this is the threshold but the current CO2 concentration is 387 ppm indicating that we have already surpassed the threshold. The article also indicates that no more than 11 million tonnes of phosphorous should be entering oceans per year. One of the major points in the article is that all the boundaries are closely related to one another, in other words if one boundary is crossed than the other boundaries are also likely to be crossed. If the thresholds of these boundaries are maintained then Earth will continue to be a safe place to live however if these thresholds are continuously surpassed then humanity is in danger.
Do new questions arise from the results?
The appropriate threshold for N2 is still unclear, indicating that more resesarch is needed to accurately pinpoint a value. So far, seven boundaries have been established but only some have concrete evidence and information. This indicates that more studies need to be done to describe the link between these boundaries. The article also does not really indicate how disturbing one boundary might affect another one.
Were there any specific challenges or advantages in understanding the paper (e.g. did the authors provide sufficient background information to understand experimental logic, were methods explained adequately, were any specific assumptions made, were conclusions justified based on the evidence, were the figures or tables useful and easy to understand)?
A major problem with this article was that the methodologies were not properly and clearly explained. They mostly stated the results without clearly indicating how they got the results, and this makes their work seem less valid. Another flaw is that they did not include any useful figures, tables or graphs. Adding these would have greatly helped in understanding the concepts. Other than this the claims and conclusions made in this paper were well supported and all the points were justified with proper evidence. The provided background was also sufficient to understand the topic. The different sections within the paper were divided strategically which made it easy to follow along.
Describe the numerical abundance of microbial life in relation to the ecology and biogeochemistry of Earth systems.
What are the primary prokaryotic habitats on Earth and how do they vary with respect to their capacity to support life? Provide a breakdown of total cell abundance for each primary habitat from the tables provided in the text.
There are three primary prokaryotic habitats on Earth inlcuding the open ocean, soil and subsurface sediements. The open ocean has approximately 1.181x10^29 cells, and prokaryotes are primarily found in the upper 200m of open ocean. The soil has approximately 2.556x10^29 cells and subsurface sediments have about 3.8x10^30 cells.
What is the estimated prokaryotic cell abundance in the upper 200 m of the ocean and what fraction of this biomass is represented by marine cyanobacterium including Prochlorococcus? What is the significance of this ratio with respect to carbon cycling in the ocean and the atmospheric composition of the Earth?
The estimated prokaryotic cell abundance in the upper 200m of the ocean is 3.6x10^28 cells at ocean density of 5x10^5 cells/mL. The abundance of autotrophs is 2.9x10^27 cells and the density of Procholorococcus is 4x10^4 cells/mL. In this habitat the average cellular density is 8% which is calculated by:
(4*10^4 cells/ml) divided by (5x10^5 cells) times 100%= 8%
8% of the autotrophs are responsible for the amount of carbon being cycles through the Earth’s oceans which supports the carbon availability for the rest of the 92% heterotrophs present.
What is the difference between an autotroph, heterotroph, and a lithotroph based on information provided in the text?
The article states that autotrophs use simple compounds around them to make their own complex organic compound. Autotrophs are “self-nourishing” and fix inorganic carbon (CO2) into their biomass. Heterotrophs assimilate organic carbon to produce energy. Lithotrophs use inorganic substrates to produce energy.
Based on information provided in the text and your knowledge of geography what is the deepest habitat capable of supporting prokaryotic life? What is the primary limiting factor at this depth?
There is life up to 4km deep in the subsurface and the deepest point in the ocean is the Mariana’s Trench which is about 10.9km deep. Therefore the lowest point where life could potentially exist is 14.9km deep. The limiting factor at this depth could be the high temperature as it reaches 125degrees Celcius which is the very close to the upper temperature limit for prokaryotic life. There is also limited oxygen availability and sunlight at these depths which could also be limiting factors. The change in temperature per depth is roughly 22 degrees celcius/km.
Based on information provided in the text your knowledge of geography what is the highest habitat capable of supporting prokaryotic life? What is the primary limiting factor at this height?
The highest point on Earth where life exists is Mount Everest which is about 8.8km. However, prokaryotes have been detected in the atmosphere at altitudes as high as 57-77 km. The limiting factors can include the presence and absence of certain gasses such as oxygen, nitrogen, that are required by some prokaryotes to grow. Temperature can also be a limiting factor as it drops dramatically with altitude. The lack of moisture and presence of ionizing radiation at high altitudes can inhibit the survivial of prokaryotes.
Based on estimates of prokaryotic habitat limitation, what is the vertical distance of the Earth’s biosphere measured in km?
An accurate range may be from be top of Mount Everest (8.8km high) to the bottom of Mariana’s Trench ( 10.9km deep), with an additional 4km deeper.Thus the vertical range of the biosphere is approximately 24km.
How was annual cellular production of prokaryotes described in Table 7 column four determined? (Provide an example of the calculation)
Annual cell production=(population) * (number of days in a year)(turnover time/year)= ____ cells/year
Sample Calulation of marine heterotrophs: (3.6x10^28 cells )(365 days)*(16 turnovers)= 8.2x10^29 cells/year
What is the relationship between carbon content, carbon assimilation efficiency and turnover rates in the upper 200m of the ocean? Why does this vary with depth in the ocean and between terrestrial and marine habitats?
Carbon assimilation efficiency assumption: 0.2(20%) converting organic carbon into biomass Carbon content: 20x10^-30 Pg
Turnover rates: 8.2x10^29 cells/year Number of cells: 3.6x10^30 cells
Carbon content calculation: (3.6x10^28 cells)*(20x10^-30 Pg/cell)= 0.72 Pg of carbon in marine heterotrophs (total amount of cells and amount of carbon per cell)
4x0.72=2.88 Pg/yr —> They should have technically done 5x0.72 (The multiplier should be 5 because the assimilation efficiency is 20%). They used a multiplier of 4 instead maybe because they are accounting for some sort of loss along the way.
A large population will have a higher carbon content and longer turnover. As a result, carbon content is highly dependent on turnover rate and population size assuming that the estimated carbon assimilation efficiency is constant. These values will differ depending on the amount of exposure to sunlight and the presence of lytic bacteriophages that are present in large amounts within the upper 200km of the ocean.
51 Pg/year x 85% consumed = 43 Pg/year consumed per year
(43 Pg/year)/2.88 Pg/year= 14.9 turnover every 24.5 days
How were the frequency numbers for four simultaneous mutations in shared genes determined for marine heterotrophs and marine autotrophs given an average mutation rate of 4 x 10-7 per DNA replication? (Provide an example of the calculation with units. Hint: cell and generation cancel out)
4x10^-7 mutations/generation
(4x10-7)4= 2.56x10^-26 mutations per generation —> have to go to the power of 4 since there are 4 mutations in a single gene at the same time
Next… we need to know about turnover to realize if this is a often or rare event. How many times do cells generate themselves per year. (365 days)/16) = 22.8 turnovers /year
(3.6x10^28 cells )22.8= 8.2x10^29 cells/year
(8.2x10^29 cells/year) ( 2.56x10^-26 mutationns/generation) = 22.1x10^4 mutation/year
Given the large population size and high mutation rate of prokaryotic cells, what are the implications with respect to genetic diversity and adaptive potential? Are point mutations the only way in which microbial genomes diversify and adapt?
The high mutation rate of prokaryotic cells indicates there is potential for high genetic diversity as these mutations cause individual prokaryotes to be genetically different from others. The mutations that increase fitness and survival for the prokaryotes will be able to adapt to their surroundings and successfully pass the mutations to the next generation. Apart from point mutations, horizontal gene transfer that occurs between prokaryotic organisms can also introduce new genetic material which increases genetic diversity.
What relationships can be inferred between prokaryotic abundance, diversity, and metabolic potential based on the information provided in the text?
The high prokaryotic abundance allows for high genetic diveristy. Thi is because even if some mutations decrease the fitness and survival rate of prokaryotes, there is stil a large enough population present to continue reproducing without wiping out the existence of prokaryotes altogether. Also the large enough population and diversity allows for more increased metabolic potential.
Discuss the role of microbial diversity and formation of coupled metabolism in driving global biogeochemical cycles
What are the primary geophysical and biogeochemical processes that create and sustain conditions for life on Earth? How do abiotic versus biotic processes vary with respect to matter and energy transformation and how are they interconnected?
Tectonic and atmospheric photochemical processes supply substrates, remove products to create geochemical cycles. Both of these processes allows elements and molecules to interact with one another causing molecules to interact with each other and reach thermodynamic equilibruim. The biogeochmeical processes include microbially catlyzed, tthermodynamically constrained redox reactions and acid/base reactions. Rock weathering drives nutrient cycels to remove CO2 and allow other biological processes to occur. Volcanism and microbial-catalyzed redox reactions are also important for the fluxes of major bioelements including C, H, O, N, S and P. Abiotic processes create biogeochemical cycles in a planetary scale and geological time scales and they affect carbon, sulphur and phosphorus levels on Earth. Biotic processes on the other hand are driven by redox reactions and are responsible for carbon, hydrogen, nitrogen and sluphur. The biogeochemical cycles have evolved to form abiotically drived acid/base and biologically drived redox reactions, which set lower limits one external energy to sustain these cycles.
Why is Earth’s redox state considered an emergent property?
The Earth’s redox state is an emergent property because the feedback between microbial evolution and biogeochemical processes have created the current redox state of the Earth. All of these processes are linked and interconnected in some way.
How do reversible electron transfer reactions give rise to element and nutrient cycles at different ecological scales? What strategies do microbes use to overcome thermodynamic barriers to reversible electron flow?
A nutrient cycle is produced when the products of one reaction are fed into a new reaction, and these cycles can be either oxidative or reductive. As for strategies methanogenic Archae that reduce CO2 with H2 also require high H+ tension for the reaction to proceed forward. Without the input of H+, the reaction will proceed in reverse. Certain species of methanogens use this reverse reaction through the sunergistic cooperation with H2 consuming sulfate reducers.
Using information provided in the text, describe how the nitrogen cycle partitions between different redox “niches” and microbial groups. Is there a relationship between the nitrogen cycle and climate change?
In order for organisms to have access to N2 for synthesis of proteins and nucliec acids, nitrogen fixation has to occur. Nitrogen fixation converts N2 to NH4. However, the enzymes that are resposible for nitrogen fixation are inhibited by the presence of O2. In the presence of O2, NH4 is oxidized to nitrite by a group of bacteria. The nitrite is then further oxidized to nitrate by a different set of nitrifying organisms. These organisms perform reactions that reduce CO2 to organic matter. On the other hand, in the absence of O2, microbes can use nitrite and nitrate as electron acceptors in anaerobic oxidation leading to N2 prodution, and this completes the Nitrogen cycle. The nitrogen cycle forms an interdependent electron pool that requires oxygen produced from photosynethesis and the presence of organic matter. Changes in the climate can have a direct effect on photosynthesis which can in turn affect the Nitrogen cycle. This is because photosynthetic organisms requrie nitrogen oxides as terminal electron acceptors and these cannot be supplied if the nitrogen cycle is flawed. The Nitrogen cycle can also influence climate change by decreasing CO2 levels. Nitrifying organisms can use NH4 or NO2 to reduce CO2 into organic matter which will in turn decrease CO2 levels in the atmosphere.
What is the relationship between microbial diversity and metabolic diversity and how does this relate to the discovery of new protein families from microbial community genomes? There is a lot of metabolic diversity among microbial communities. The discovery of new protein families is increasing with the number of new genomes that are sequenced. Several essential multimeric microbial engines are conserved even though they are operating sub-optimally. This causes the generation of complicated repair cycles where new proteins can be created to either repair or replace the sub-optimally performing protein. So the conservation of such essential metabolic genes can cause new protein families to arise.
On what basis do the authors consider microbes the guardians of metabolism? Life was very restricted due to the glacial periods and as a result metabolic pathways have been protected. Since the metabolic mechanisms have been transferred by horizontal gene transfer to all species on earth, it is possible for individual taxonomic units to go extint while the core metabolic processes continue to persist.
NOTE: I had a meeting with Dr. Hallam on April 12, and I recieved a 4.5/5 on my initial essay. I have made all the edits he asked me to make to increase my mark. Below is the essay that Dr. Hallam read and provided feedback on. ,
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